HUDSON — A battle between Columbia County District Attorney Paul Czajka and local court judges over who controls plea bargains is causing a backlog of cases, and some defendants are being ordered to court by justices even though charges have been dropped.

Shortly after being elected last year, Czajka wrote a letter to town and village justices in the county saying his office would handle all cases and pleas.

Czajka, a former county judge and a Republican, said he made a campaign promise to streamline prosecutions in the county's municipal courts.

"I am proud to say I get along with all of the judges in Columbia County very well and professionally, but from time to time we have disagreements," Czajka said. "It is an adversarial system and judges are not supposed to be adversarial, but I am."

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The cases at issue are mostly vehicle-and-traffic violations and low-level misdemeanors, cases that in the past were often resolved by arresting officers or the justices themselves, especially traffic offenses.

It is common for judges to go along with plea deals involving lesser charges and reduced sentences if an agreement is reached between the prosecutor and the defense attorney. If, however, there is no deal and a defendant wants to plead to the original charge, judges may have some discretion in sentencing.

Czajka notified justices that all plea deals, sentences and decisions on whether to even prosecute are solely under the jurisdiction of his office.

These demands have spawned a rebellion in some local courts.

Taghkanic Town Court Justice Jeffrey S. Tallackson fired off a stern letter to the district attorney on June 14, telling him "While the people may make whatever recommendation they wish, sentencing is the court's prerogative, not the people's — the court is not a rubber stamp."

Tallackson's letter is one of several between the courts and Czajka that were obtained by the Times Union.

The district attorney said the justices are overreaching. "If attorneys and judges agreed on everything, we would not need judges," Czajka said.

Czajka and some judges also are at odds over who has the final say about whether charges should be dropped against a defendant, an outcome more common in the lower courts.

This disagreement prompted some justices to keep cases on their calendars and order defendants to appear in court even though the district attorney has notified the defendant that he would drop their charges and would not be in court.

The legal imbroglio has placed 63 cases in Kinderhook Village Court on hold while Czajka tries to have Village Justice David Dellehunt removed from hearing cases prosecuted by his office.

"Not only has Judge Dellehunt interfered with the people's discretion in his own court he has attempted to convince other judges that the district attorney has no authority to decline to prosecute matters and, further, that we have no authority to place conditions on plea bargains," Czajka wrote in asking for Dellehunt's recusal.

Dellehunt, who works full time as a clerk for state Supreme Court Justice George Ceresia, has so far declined to give up his cases. He would not discuss the matter with the Times Union.

Czajka claims the judge should be barred from hearing his cases because of an alleged bias against him. "On April 21, 2004, then- County Attorney David Dellehunt publicly stated about me (then a judge) that I had a 'general lack of civility towards lawyers,' as well as 'everyone else who enters my courtroom,'" according to Czajka.

Czajka wrote that state legal rules forbid officers of the court from publicly criticizing one another. He cited the case of Albany County District Attorney David Soares' censure for critical comments he made about Judge Stephen Herrick's 2010 decision, later overturned, to remove the district attorney's office from the prosecution of a steroids case. Soares called the decision a "get-out-of-jail-free card for every criminal defendant in New York state."

Attorney and court observer Eugene Keeler, a Democrat, former Columbia County district attorney and public defender who lost to Czajka in November, was critical of the district attorney's actions.

"Mr. Czajka's behavior is putting the county's public safety at risk by failing to vigorously prosecute cases for inconsequential reasons," Keeler said. "He's also harming victims by not giving them the quick justice which they deserve."

Though the situation has caused their clients unnecessary court appearances, legal expenses and delays, several defense attorneys were reluctant to discuss the dispute and the impact it is having on the flow of cases in the local courts.

Chatham Town Court Justices James Borgia-Forster and Jason Shaw let their positions be known in a July 16 letter to Czajka.

"The legal memorandum from the 3rd Judicial District circulated several months ago concluded that a district attorney did not have authority to withdraw pending accusatory instruments," they wrote.

That letter follows one sent five days earlier by Czajka to Tallackson. "I have indeed submitted and I continue to submit, directly or through assistant district attorneys, the district attorney has unfettered discretion to determine whether or not to prosecute an individual and the courts may not and should not interfere with that discretion," Czajka wrote.